[BioC] edgeR adding RefSeq IDs

[Robin [guest]]

My pipeline for adding annotations suddenly didn't work, maybe because some packages are updated. Could you check if something is wrong with my pipeline, I loose all the rows when I add annotations:

> data <- read.table("~/Documents/Jobb/mRNA_Ch12/TreatedControlCounts.csv", row.names=1, sep="", header=T)
> head(data)
             T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h C0h C0.25h C0.5h C1h C2h C3h
NM_001001130  68     95    56  43  66  62  68   90   63   89  65     85    58  49  81  49
NM_001001144   0      1     4   0   1   1   1    4    1    2   1      3     1   0   6   3
NM_001001152  79    129    52  50  24  45 130  154  112  147  56     85    67  33  52  31
NM_001001160   1      1     2   0   0   1   0    0    0    1   0      1     2   4   2   1
NM_001001176   0      0     0   0   0   0   0    0    0    0   0      0     0   0   0   0
NM_001001177   1      3     2   3   0   1   1    0    2    0   1      6     4   1   3   0
             C6h C12h C24h C48h
NM_001001130  76   73   48   77
NM_001001144   0    1    2    1
NM_001001152  93   77   65  109
NM_001001160   0    2    1    0
NM_001001176   0    0    0    0
NM_001001177   0    3    0    2
> y <- DGEList(counts=data[,1:20], genes=data[,0:1])
> library(org.Mm.eg.db)
> idfound <- rownames(y$genes) %in% mappedRkeys(org.Mm.egREFSEQ)
> y <- y[idfound,]
> dim(y)
[1]  0 20
> egREFSEQ <- toTable(org.Mm.egREFSEQ)
> m <- match(rownames(y$genes), egREFSEQ$accession)
> y$genes$EntrezGene <- egREFSEQ$gene_id[m]
> y$genes$Symbol <- egSYMBOL$symbol[m]
> m <- match(y$genes$EntrezGene, egSYMBOL$gene_id)
> y$genes$Symbol <- egSYMBOL$symbol[m]
> head(y$genes)
[1] genes      EntrezGene Symbol    
<0 rows> (or 0-length row.names)

 -- output of sessionInfo(): 

> sessionInfo() 
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edgeR_3.4.0           limma_3.18.0          GSEABase_1.24.0      
 [4] annotate_1.40.0       org.Mm.eg.db_2.10.1   AnnotationForge_1.4.0
 [7] org.Hs.eg.db_2.10.1   GOstats_2.28.0        graph_1.40.0         
[10] Category_2.28.0       GO.db_2.10.1          RSQLite_0.11.4       
[13] DBI_0.2-7             Matrix_1.0-14         lattice_0.20-24      
[16] AnnotationDbi_1.24.0  Biobase_2.22.0        BiocGenerics_0.8.0   

loaded via a namespace (and not attached):
 [1] genefilter_1.44.0 grid_3.0.2        IRanges_1.20.0    RBGL_1.38.0      
 [5] splines_3.0.2     stats4_3.0.2      survival_2.37-4   tools_3.0.2      
 [9] XML_3.98-1.1      xtable_1.7-1 

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